Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

Genome-Wide Analysis Of miRNAs In Brachypodium distachyon

Skye A. Schmidt¹ , Dong-Hoon Jeong¹ , Linda A. Rymarquis¹ , Monica Accerbi¹ , Sunhee Park¹ , Marcelo A. German² , Matthias Gannesman¹ , Jixian Zhai¹ , Emanuele DePaoli¹ , Sai Guna Ranjan Gurazada ¹ , Blake C. Meyers¹ , Pamela J. Green¹

¹  Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE, 19711, USA

²  Dow AgroSciences LLC, 16160 SW Upper Boones Ferry Road, Portland, OR, 97224, USA

miRNAs are small, endogenous RNAs that post-transcriptionally regulate gene expression in nearly all eukaryotic systems. In plants, miRNAs can serve as major regulators of development, stress responses, metabolism, and other processes through the miRNA-guided cleavage of specific target RNAs. While miRNAs and their target interactions are well-characterized in systems such as Arabidopsis and rice, little is known about their roles in others including temperate grasses and potential biofuel crops. In this study, we use next-generation sequencing technology to identify miRNAs in different tissues and following abiotic stress treatments of Brachypodium distachyon, a rapidly developing model system for temperate grasses and biofuel crops. A total of more than 64 million reads were obtained from 12 small RNA libraries, resulting in an average of more than 1.4 million distinct genome-matched small RNA sequences per library, from which both conserved and new miRNAs have been identified. The data also indicate new cases of miRNA regulation likely to influence the cleavage of their targets. To identify miRNA targets on a global scale, we use an approach called Parallel Analysis of RNA Ends (PARE) that facilitates the sequencing of 3’ products of miRNA-guided target RNA cleavage. Because miRNAs and their targets can form missing links in many important gene regulatory networks, the identification of miRNA and target RNA pairs in Brachypodium will help to better understand how small RNAs contribute to the regulation of genes and genomes. This work was funded by the Plant Feedstock Genomics for Bioenergy Program of the DOE.